Food restricted transgenic coho salmon
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR673469_1.fastq.gz | Fastqsanger.gz | |||
| ERR673469_2.fastq.gz | Fastqsanger.gz | |||
| ERR673470_1.fastq.gz | Fastqsanger.gz | |||
| ERR673470_2.fastq.gz | Fastqsanger.gz | |||
| ERR673471_1.fastq.gz | Fastqsanger.gz |
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Project description:The aim of this sequencing experiment was to make available liver tissue expression for selected fish species, northern pike (Esox lucius, Eluc), coho salmon (Oncorhynchus kisutch, Okis) and Arctic charr (Salvelinus alpinus, Salp), for comparative expression studies between the species. Samples in replicate of four were sacrificed according to protocols at each of the facilities from where samples were obtained. RNA was extracted from samples and Illumina TruSeq Stranded mRNA libraries were built. Sequencing was performed in two passes on an Illumina HiSeq2500, paired-end 125bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the NCBI genomes of the respective species using STAR and gene level counting using RSEM and NCBI gene annotation.
2020-04-30 | E-MTAB-8962 | biostudies-arrayexpress
Project description:Background: Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. Results: We characterised the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12h, 24h, 36h, 48h, and 60h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. Conclusions: Our results highlight the key role of keratinocytes in coho salmon’s sea lice resistance, and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.
2024-06-24 | GSE269132 | GEO
Project description:Most Pacific salmonids undergo smoltification and transition from freshwater to saltwater. Saltwater acclimation requires salmonids to make various adjustments in color, shape, size, metabolism, catabolism, and osmotic and ion regulation. The molecular mechanisms underlying this transition are largely unknown. The present study acclimated coho salmon (Oncorhynchus kisutch) to four different salinities (<0.5, 8, 16, and 32 ppth) and assessed gene expression through microarray analysis of gill, liver and olfactory tissues. Gills are involved in osmotic regulation, liver plays a role in energetics, and olfactory tissues are involved in behavior. Between all salinity treatments, liver had the highest number of differentially expressed genes at 1,616. Gills had 1,074 differentially expressed genes and olfactory tissue had 924. The difference in the number of differentially expressed genes may be due to the higher responsiveness of liver to metabolic changes after salinity acclimation to provide energy to fuel other metabolic and osmoregulatory tissues like gills. Differentially expressed genes were tissue and salinity treatment dependent. There were no genes differentially expressed in all salinity treatments and all three tissues. Five genes were targeted for microarray confirmation by qPCR and included CCAAT/enhancer binding protein ? (CEBPB), calpain 1 (CAPN1), proto-oncogene, serine/threonine kinase (Pim1), aldolase B, fructose-bisphosphate (aldob), and complement component 3 (c3). qPCR expression profiles of these genes matched array outputs. Gene ontology term analysis revealed biological processes, molecular functions, and cellular components that were significant. Most terms were tissue dependent. For liver, oxygen binding and transport terms were highlighted, suggesting possible impacts on metabolism. For gills, muscle and cytoskeleton related terms were emphasized and for olfactory tissues, immune response related genes were accentuated. Interaction networks were examined in combination with GO terms and determined similarities between tissues for potential osmosenors and signal transduction cascades. Overall this study suggests that Pacific salmonids share many salinity acclimation molecular mechanisms with other species, with a few new genes identified, and that although the three tissues shared certain underlying mechanism, many of the differentially expressed genes were tissue-specific. To assess how salinity acclimation in coho salmon (Oncorhynchus kisutch) impacted gene expression in gills, liver, and olfactory tissues.
2016-03-22 | E-GEOD-67461 | biostudies-arrayexpress
Project description:Fast growth is vital to the commercial production of fish and has been achieved gradually, through generations of selective breeding, and instantaneously, through growth hormone (GH) transgenesis (GHT). The proteomic basis for these differing routes towards a largely common higher phenotype is poorly characterized, as are associated implications for fish health parameters. We addressed this knowledge gap in coho salmon (Oncorhynchus kisutch) testing two hypotheses: i) that selective breeding and GHT are underpinned by both parallel and non-parallel changes in growth pathways compared to wild-type, and ii) that rapidly growing fish have less scope to allocate energetic resources into immune function. Skeletal muscle was studied, owing to its central role in growth and energetic storage. We compared the proteomes of GHT and growth-selected domesticated strains with wild-type animals following injections with PBS (control) and Poly I:C (to mimic viral infection). Hybrid quadrupole-Orbitrap mass-spectrometry using a label-free analysis revealed large changes in the proteome of GHT and growth-selected strains that were strikingly non-overlapping, with surprisingly few parallel changes. GHT was characterized by a focal upregulation of translation systems, while growth-selected fish presented a larger and more diverse set of changes, consistent with genetic alterations influencing an array of metabolic and cellular pathways. Contrasting past studies examining mRNA levels, many proteomic changes distinguished the growth-selected strain from both GHT and wild fish. Contrasting our second hypothesis, Poly I:C had little detectable effect on the muscle proteome. This investigation reveals that highly distinct proteome profiles can explain outwardly similar growth phenotypes, improving our understanding of how fast growth is achieved in animal strains created by humans.
2018-09-24 | PXD009537 | Pride
Project description:Coho Salmon GH Transgenic Study Keywords: other
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Project description:There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.
2019-12-03 | GSE123307 | GEO
Project description:There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.
2019-12-03 | GSE123306 | GEO
Project description:There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.
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Project description:There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.
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Project description:Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments
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